Let’s get everyone up an running with Klone and RStudio.

Log in

sr320@Stevens-MacBook-Air-184 ~ % ssh sr320@klone.hyak.uw.edu
(sr320@klone.hyak.uw.edu) Password: 
(sr320@klone.hyak.uw.edu) Duo two-factor login for sr320

Enter a passcode or select one of the following options:

 1. Duo Push to XXX-XXX-3626
 2. Duo Push to iOS
 3. Phone call to XXX-XXX-3626

Passcode or option (1-3): 1

CD to srlab directory

cd /gscratch/srlab/

Create user directory in srlab (if not present)

mkdir sr320

Add containers to your local directory

-rwxr-xr-x 1 samwhite all   3311583232 2024-12-04 srlab-bioinformatics-container-09dfcb2.sif
-rwxrwxr-x 1 samwhite srlab 2985074688 2024-10-17 srlab-bioinformatics-container-2bd5d44.sif
-rwxr-xr-x 1 samwhite all   3008335872 2024-11-06 srlab-bioinformatics-container-586bf21.sif
-rwxr-xr-x 1 samwhite all   3008442368 2024-11-07 srlab-bioinformatics-container-f4142f4.sif
-rwxr-xr-x 1 samwhite all   3380895744 2025-01-04 srlab-R4.4-bioinformatics-container-703094b.sif

Specifically srlab-R4.4-bioinformatics-container-703094b.sif

#within user directory
cp ../containers/srlab-R4.4-bioinformatics-container-703094b.sif .

See Footnotes for more information on containers.

Warning

Users should add the following line in ~/.Renviron. If you don’t have a ~/.Renviron, you can create it like this: touch ~/.Renviron

R_LIBS_USER in ~/.Renviron. Example:

cat ~/.Renviron
# Set local library installation path
R_LIBS_USER=/gscratch/srlab/${USER}/R_libs_apptainer

This configuration directs R to install and access packages from a custom directory rather than the system-wide library, which is especially useful in shared or containerized environments.

SLURM JOB SCRIPT

cp ../sr320/rstudio-server.job .

Warning

User needs to (maybe) set/change the following in the SLURM script before starting script:
- #SBATCH --partition=
- #SBATCH --time=
- #SBATCH --cpus-per-task=
- #SBATCH --mem=
- #SBATCH --chdir=
- RSTUDIO_CWD="/gscratch/srlab/sr320" # UPDATE THIS LINE
- RSTUDIO_SIF="srlab-R4.4-bioinformatics-container-703094b.sif" # UPDATE THIS LINE

Partition Options

cpu-g2-mem2x or ckpt

[sr320@klone-login03 containers]$ hyakalloc
       Account resources available to user: sr320        
╭─────────┬──────────────┬──────┬────────┬──────┬───────╮
│ Account │    Partition │ CPUs │ Memory │ GPUs │       │
├─────────┼──────────────┼──────┼────────┼──────┼───────┤
│   srlab │ cpu-g2-mem2x │   32 │   490G │    0 │ TOTAL │
│         │              │   12 │   100G │    0 │ USED  │
│         │              │   20 │   390G │    0 │ FREE  │
╰─────────┴──────────────┴──────┴────────┴──────┴───────╯
 Checkpoint Resources  (ckpt)
╭───────┬──────┬──────╮
│       │ CPUs │ GPUs │
├───────┼──────┼──────┤
│ Idle: │ 4557 │  148 │
╰───────┴──────┴──────╯

Open

nano rstudio-server.job

#!/bin/sh

#SBATCH --job-name=rstudio-server
#SBATCH --account=srlab
#SBATCH --partition=cpu-g2-mem2x #update this line - use hyakalloc to find partitions you can use
#SBATCH --time=15-08:00:00
#SBATCH --ntasks=1              # Number of tasks
#SBATCH --cpus-per-task=12     # Increased threads from 4 to 8
#SBATCH --nodes=1
#SBATCH --mem=100G
#SBATCH --signal=USR2
#SBATCH --output=%x_%j.out
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/srlab/sr320

# This script will request a single CPU with four threads with 20GB of RAM for 2 hours. 
# You can adjust --time, --nodes, --ntasks, and --mem above to adjust these settings for your session.

# --output=%x_%j.out creates a output file called rstudio-server_NNNNNNNN.out 
# where the %x is short hand for --job-name above and the N's are an 8-digit 
# jobID assigned by SLURM when our job is submitted.

RSTUDIO_CWD="/gscratch/srlab/sr320" # UPDATE THIS LINE
RSTUDIO_SIF="srlab-R4.4-bioinformatics-container-703094b.sif" # UPDATE THIS LINE


# Create temp directory for ephemeral content to bind-mount in the container
RSTUDIO_TMP=$(/usr/bin/python3 -c 'import tempfile; print(tempfile.mkdtemp())')

mkdir -p -m 700 \
        ${RSTUDIO_TMP}/run \
        ${RSTUDIO_TMP}/tmp \
        ${RSTUDIO_TMP}/var/lib/rstudio-server

cat > ${RSTUDIO_TMP}/database.conf <<END
provider=sqlite
directory=/var/lib/rstudio-server
END

# Set OMP_NUM_THREADS to prevent OpenBLAS (and any other OpenMP-enhanced
# libraries used by R) from spawning more threads than the number of processors
# allocated to the job.
#
# Set R_LIBS_USER to a path specific to rocker/rstudio to avoid conflicts with
# personal libraries from any R installation in the host environment

cat > ${RSTUDIO_TMP}/rsession.sh <<END
#!/bin/sh

export OMP_NUM_THREADS=${SLURM_JOB_CPUS_PER_NODE}
export R_LIBS_USER=${RSTUDIO_CWD}/R
exec /usr/lib/rstudio-server/bin/rsession "\${@}"
END

chmod +x ${RSTUDIO_TMP}/rsession.sh

export APPTAINER_BIND="${RSTUDIO_CWD}:${RSTUDIO_CWD},/gscratch:/gscratch,${RSTUDIO_TMP}/run:/run,${RSTUDIO_TMP}/tmp:/tmp,${RSTUDIO_TMP}/database.conf:/etc/rstudio/database.conf,${RSTUDIO_TMP}/rsession.sh:/etc/rstudio/rsession.sh,${RSTUDIO_TMP}/var/lib/rstudio-server:/var/lib/rstudio-server"

# Do not suspend idle sessions.
# Alternative to setting session-timeout-minutes=0 in /etc/rstudio/rsession.conf
export APPTAINERENV_RSTUDIO_SESSION_TIMEOUT=0

export APPTAINERENV_USER=$(id -un)
export APPTAINERENV_PASSWORD=$(openssl rand -base64 15)

# get unused socket per https://unix.stackexchange.com/a/132524
# tiny race condition between the python & apptainer commands
readonly PORT=$(/mmfs1/sw/pyenv/versions/3.9.5/bin/python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()')
cat 1>&2 <<END
1. SSH tunnel from your workstation using the following command:

   ssh -N -L 8787:${HOSTNAME}:${PORT} ${APPTAINERENV_USER}@klone.hyak.uw.edu

   and point your web browser to http://localhost:8787

2. log in to RStudio Server using the following credentials:

   user: ${APPTAINERENV_USER}
   password: ${APPTAINERENV_PASSWORD}

When done using RStudio Server, terminate the job by:

1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window)
2. Issue the following command on the login node:

      scancel -f ${SLURM_JOB_ID}
END

source /etc/bashrc
module load apptainer

apptainer exec --cleanenv --home ${RSTUDIO_CWD} ${RSTUDIO_CWD}/${RSTUDIO_SIF} \
    rserver --www-port ${PORT} \
            --auth-none=0 \
            --auth-pam-helper-path=pam-helper \
            --auth-stay-signed-in-days=30 \
            --auth-timeout-minutes=0 \
            --rsession-path=/etc/rstudio/rsession.sh \
            --server-user=${APPTAINERENV_USER}

APPTAINER_EXIT_CODE=$?
echo "rserver exited $APPTAINER_EXIT_CODE" 1>&2
exit $APPTAINER_EXIT_CODE

Run

sbatch rstudio-server.job

Folllow Instructions in output file to connect to RStudio.

1. SSH tunnel from your workstation using the following command:

   ssh -N -L 8787:n3263:56093 sr320@klone.hyak.uw.edu

   and point your web browser to http://localhost:8787

2. log in to RStudio Server using the following credentials:

   user: sr320
   password: PDQlr876755PgP3g37c

When done using RStudio Server, terminate the job by:

1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window)
2. Issue the following command on the login node:

      scancel -f 24359989

Footnotes

srlab-bioinformatics-container-<git commit hash>.sif: A "catch-all" container which holds most of the commonly used bioinformatics software
used by the Roberts Lab. The <git commit hash> is taken from the definition file used to construct the container. The definition file can be found at
/gscratch/srlab/gitrepos/RobertsLab/code/apptainer_definition_files/srlab-bioinformatics-container.def.

Definition File

[sr320@klone-login03 containers]$ cat /gscratch/srlab/gitrepos/RobertsLab/code/apptainer_definition_files/srlab-bioinformatics-container.def

# NOTE:
# To use RepeatMasker with this container, RepeatMasker must be installed on the local computer in the following location:
#
# /gscratch/srlab/programs/RepeatMasker
# 
# RepeatMasker must be configured on the local computer prior to running via this container.
# The container expects the following files:
#
# /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/dfam38_full.0.h5
# /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/rmlib.config


Bootstrap: docker
From: rocker/rstudio:4.4.1
%files
    # Load file with R package installation commands in to container at /tmp
    # Expects file called "r_packages_installs.R" to be in current directory.
    r_packages_installs.R /tmp/

%setup


%environment
    ### Set program locations/versions for system PATH ###
    programs_location="/srlab/programs"
    bismark_version="0.24.2"
    bowtie2_version="2.5.4"
    diamond_version="2.1.9"
    fastp_version="0.23.4"
    fastqc_version="0.12.1"
    gffcompare_version="gffcompare-0.12.6"
    hisat2_version="2.2.1"
    kallisto_version="0.51.1"
    miniforge_version="24.7.1-0"
    multiqc_version="1.24.1"
    ncbi_blast_version="2.16.0"
    ncbi_datasets_version="13.34.0"
    repeatmasker_version="4.1.7-p1"
    rmblast_version="2.14.1"
    salmon_version="1.10.0"
    samtools_version="1.20"
    stringtie_version="2.2.1"
    trimmomatic_version="0.39"

    mamba_envs_dir="${programs_location}/miniforge3-${miniforge_version}/envs"

    ######################################################

    export LC_ALL=C
    
    ### Set container system PATH ###
    PATH="/usr/local/sbin:\
/usr/local/bin:\
/usr/sbin:\
/usr/bin:\
/sbin:\
/bin:\
${programs_location}:\
${programs_location}/Bismark-${bismark_version}:\
${programs_location}/bowtie2-${bowtie2_version}-sra-linux-x86_64:\
${programs_location}/fastqc-${fastqc_version}:\
${programs_location}/${gffcompare_version}:\
${programs_location}/hisat2-${hisat2_version}:\
${programs_location}/kallisto-${kallisto_version}/build/src:\
${programs_location}/miniforge3-${miniforge_version}/bin:\
${mamba_envs_dir}/multiqc_env/bin:\
${programs_location}/ncbi-blast-${ncbi_blast_version}+/bin:\
${programs_location}/ncbi-datasets-${ncbi_datasets_version}:\
${programs_location}/RepeatMasker:\
${programs_location}/rmblast-${rmblast_version}/bin:\
${programs_location}/salmon-latest_linux_x86_64/bin:\
${programs_location}/samtools-${samtools_version}:\
${programs_location}/stringtie-${stringtie_version}.Linux_x86_64:\
${programs_location}/Trimmomatic-${trimmomatic_version}:\
${programs_location}/trf409.linux64"
    ######################################################


%post
    # Install common/base libraries/dependencies
    apt update && \
    apt install -y --no-install-recommends \
    apt-utils \
    aptitude \
    automake \
    build-essential \
    bzip2 \
    cmake \
    coreutils \
    curl \
    debconf \
    default-jdk \
    dialog \
    emboss \
    gcc-multilib \
    gdebi-core \
    gfortran \
    git \
    gobjc++ \
    hmmer \
    htop \
    infernal \
    libapparmor1 \
    libbz2-dev \
    libc6 \
    libcurl4-openssl-dev \
    libedit2 \
    libfontconfig1 \
    liblzma-dev \
    libncurses5-dev \
    libncurses-dev \
    libncursesw5-dev \
    libpango1.0-dev \
    libpng-dev \
    libreadline-dev \
    libsm6 \
    libsparsehash-dev \
    libssl-dev \
    liburi-escape-xs-perl \
    liburi-perl \
    libxml2 \
    libxrender1 \
    libz-dev \
    libbz2-dev \
    liblzma-dev \
    libxt6 \
    libxtst6 \
    libzmq3-dev \
    locales \
    locales-all \
    man \
    nano \
    ncurses-dev \
    net-tools \
    openssh-client \
    parallel \
    pkg-config \
    psmisc \
    python3 \
    python-setuptools \
    rsync \
    ruby \
    software-properties-common \
    sqlite3 \
    sudo \
    texinfo \
    tree \
    unzip \
    wget \
    xorg-dev \
    zlib1g-dev

    # Run R package installation script file
    Rscript /tmp/r_packages_installs.R

    ########## Set program versions ##########

    bedtools_version="v2.31.0"
    bismark_version="0.24.2"
    bowtie2_version="2.5.4"
    diamond_version="2.1.9"
    fastp_version="0.23.4"
    fastqc_version="0.12.1"
    gffcompare_version="gffcompare-0.12.6"
    hisat2_version="2.2.1"
    kallisto_version="0.51.1"
    miniforge_version="24.7.1-0"
    multiqc_version="1.24.1"
    ncbi_blast_version="2.16.0"
    ncbi_datasets_version="16.34.0"
    repeatmasker_version="4.1.7-p1"
    rmblast_version="2.14.1"
    salmon_version="1.10.0"
    stringtie_version="2.2.1"
    samtools_version="1.20"
    trimmomatic_version="0.39"

    ##########################################
    

    
    # Set threads for faster builds
    threads="40"

    # Make programs directory
    mkdir --parents /srlab/programs

    # Change to installation directory
    cd /srlab/programs

    #Install Miniforge (Conda/Mamba)
    wget https://github.com/conda-forge/miniforge/releases/download/${miniforge_version}/Miniforge3-${miniforge_version}-Linux-x86_64.sh
    bash Miniforge3-${miniforge_version}-Linux-x86_64.sh -b -p ./miniforge3-${miniforge_version}

    export PATH="$PATH:/srlab/programs/miniforge3-${miniforge_version}/bin"

    mamba init
    . ./miniforge3-${miniforge_version}/etc/profile.d/conda.sh

    rm Miniforge3-${miniforge_version}-Linux-x86_64.sh

    ## Configure conda channels
    conda config --add channels defaults
    conda config --add channels bioconda
    conda config --add channels conda-forge
    conda config --set channel_priority strict

    # Install bedtools
    wget https://github.com/arq5x/bedtools2/releases/download/${bedtools_version}/bedtools.static
    mv bedtools.static bedtools
    chmod a+x bedtools

    # Install Bismark
    wget https://github.com/FelixKrueger/Bismark/archive/refs/tags/v${bismark_version}.zip
    unzip v${bismark_version}.zip
    rm v${bismark_version}.zip

    # Install bowtie2
    wget https://github.com/BenLangmead/bowtie2/releases/download/v${bowtie2_version}/bowtie2-${bowtie2_version}-sra-linux-x86_64.zip
    unzip bowtie2-${bowtie2_version}-sra-linux-x86_64.zip
    rm bowtie2-${bowtie2_version}-sra-linux-x86_64.zip

    # Install DIAMOND BLAST
    wget https://github.com/bbuchfink/diamond/releases/download/v${diamond_version}/diamond-linux64.tar.gz
    tar -xzvf diamond-linux64.tar.gz
    rm diamond-linux64.tar.gz

    # Install fastp
    wget http://opengene.org/fastp/fastp.${fastp_version}
    mv fastp.${fastp_version} fastp
    chmod a+x ./fastp

    # Install FastQC
    wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${fastqc_version}.zip
    unzip fastqc_v${fastqc_version}.zip
    mv FastQC fastqc-${fastqc_version}
    rm fastqc_v${fastqc_version}.zip

    # Install gffcompare
    wget http://ccb.jhu.edu/software/stringtie/dl/${gffcompare_version}.Linux_x86_64.tar.gz
    tar -xzvf ${gffcompare_version}.Linux_x86_64.tar.gz
    rm ${gffcompare_version}.Linux_x86_64.tar.gz

    # Install HISAT2
    wget https://github.com/DaehwanKimLab/hisat2/archive/refs/tags/v${hisat2_version}.tar.gz
    tar -xzvf v${hisat2_version}.tar.gz
    cd hisat2-${hisat2_version}
    make -j ${threads}
    cd -
    rm v${hisat2_version}.tar.gz

    # Install kallisto
    wget https://github.com/pachterlab/kallisto/archive/refs/tags/v${kallisto_version}.tar.gz
    tar -xzvf v${kallisto_version}.tar.gz
    cd kallisto-${kallisto_version}
    mkdir build
    cd build
    cmake ..
    make
    cd /srlab/programs
    rm v${kallisto_version}.tar.gz

    # Install MultiQC
    mamba create -n multiqc_env multiqc=1.24.1

    # Install NCBI datasets
    mkdir --parents ncbi-datasets-v${ncbi_datasets_version}

    cd ncbi-datasets-v${ncbi_datasets_version}
    
    wget https://github.com/ncbi/datasets/releases/download/v16.34.0/linux-amd64.cli.package.zip \
    && unzip linux-amd64.cli.package.zip \
    && rm linux-amd64.cli.package.zip

    cd /srlab/programs

    # Install NCBI BLAST
    wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${ncbi_blast_version}/ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz \
    && tar -zxvpf ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz \
    && rm ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz

    # RepeatMasker conda environment with Python3 and h5py using mamba
    mamba create -n repeatmasker-env python=3.8 h5py -y

    # Install RepeatMasker
    wget https://www.repeatmasker.org/RepeatMasker/RepeatMasker-${repeatmasker_version}.tar.gz
    tar -xzvf RepeatMasker-${repeatmasker_version}.tar.gz
    rm RepeatMasker-${repeatmasker_version}.tar.gz

    ## Remove default RepeatMasker DB
    rm /srlab/programs/RepeatMasker/Libraries/famdb/*

    # Set up symlinks to RepeatMasker files on Klone
    ln -s /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/dfam38_full.0.h5 /srlab/programs/RepeatMasker/Libraries/famdb/dfam38_full.0.h5
    ln -s /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/rmlib.config /srlab/programs/RepeatMasker/Libraries/famdb/rmlib.config

    # Install RMBLAST
    wget https://www.repeatmasker.org/rmblast/rmblast-${rmblast_version}+-x64-linux.tar.gz
    tar -xzvf rmblast-${rmblast_version}+-x64-linux.tar.gz
    rm rmblast-${rmblast_version}+-x64-linux.tar.gz

    # Install salmon
    wget https://github.com/COMBINE-lab/salmon/releases/download/v${salmon_version}/salmon-${salmon_version}_linux_x86_64.tar.gz
    tar -xzvf salmon-${salmon_version}_linux_x86_64.tar.gz
    rm salmon-${salmon_version}_linux_x86_64.tar.gz

    # Install samtools
    wget https://github.com/samtools/samtools/releases/download/${samtools_version}/samtools-${samtools_version}.tar.bz2
    tar -xjvf samtools-${samtools_version}.tar.bz2
    cd samtools-${samtools_version}
    ./configure
    make -j ${threads}
    cd -
    rm samtools-${samtools_version}.tar.bz2

    # Install trimmomatic
    wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${trimmomatic_version}.zip
    unzip Trimmomatic-${trimmomatic_version}.zip
    chmod +x -R Trimmomatic-${trimmomatic_version}
    rm Trimmomatic-${trimmomatic_version}.zip

    # Install StringTie
    wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-${stringtie_version}.Linux_x86_64.tar.gz
    tar -xzvf stringtie-${stringtie_version}.Linux_x86_64.tar.gz
    rm stringtie-${stringtie_version}.Linux_x86_64.tar.gz

    # Install TRF
    wget https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64
    chmod +x trf409.linux64




%labels
    Author Sam White
    Version v0.0.5
    

%help
    This is an Apptainer definition file for an Ubuntu container containing bioinformatics software for the Roberts Lab.

--- title: "Please Klone me" description: "Getting on the Rstudio Klone Machine" categories: [hyak, hpc, rstudio] #citation: date: 02-19-2025 image: http://gannet.fish.washington.edu/seashell/snaps/Monosnap_sr320__sr320klone-login03__ssh_klone.hyak.uw.edu__9830_2025-02-20_09-08-29.png # finding a good image author: - name: Steven Roberts url: orcid: 0000-0001-8302-1138 affiliation: Professor, UW - School of Aquatic and Fishery Sciences affiliation-url: https://robertslab.info #url: # self-defined draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready! format: html: code-fold: FALSE code-tools: true code-copy: true highlight-style: github code-overflow: wrap --- ```{r setup, include=FALSE} knitr::opts_chunk$set( echo = TRUE, # Display code chunks eval = FALSE, # Evaluate code chunks warning = FALSE, # Hide warnings message = FALSE, # Hide messages fig.width = 6, # Set plot width in inches fig.height = 4, # Set plot height in inches fig.align = "center", # Align plots to the center comment = "" # Prevents appending '##' to beginning of lines in code analyses ) ``` Let's get everyone up an running with Klone and RStudio. # Log in ```{bash} sr320@Stevens-MacBook-Air-184 ~ % ssh sr320@klone.hyak.uw.edu (sr320@klone.hyak.uw.edu) Password: (sr320@klone.hyak.uw.edu) Duo two-factor login for sr320 Enter a passcode or select one of the following options: 1. Duo Push to XXX-XXX-3626 2. Duo Push to iOS 3. Phone call to XXX-XXX-3626 Passcode or option (1-3): 1 ``` # CD to srlab directory ```{bash} cd /gscratch/srlab/ ``` Create user directory in srlab (if not present) ```{bash} mkdir sr320 ``` # Add containers to your local directory ``` -rwxr-xr-x 1 samwhite all 3311583232 2024-12-04 srlab-bioinformatics-container-09dfcb2.sif -rwxrwxr-x 1 samwhite srlab 2985074688 2024-10-17 srlab-bioinformatics-container-2bd5d44.sif -rwxr-xr-x 1 samwhite all 3008335872 2024-11-06 srlab-bioinformatics-container-586bf21.sif -rwxr-xr-x 1 samwhite all 3008442368 2024-11-07 srlab-bioinformatics-container-f4142f4.sif -rwxr-xr-x 1 samwhite all 3380895744 2025-01-04 srlab-R4.4-bioinformatics-container-703094b.sif ``` Specifically `srlab-R4.4-bioinformatics-container-703094b.sif` ```{bash} #within user directory cp ../containers/srlab-R4.4-bioinformatics-container-703094b.sif . ``` See Footnotes for more information on containers. ::: callout-warning Users should add the following line in `~/.Renviron`. If you don't have a `~/.Renviron`, you can create it like this: `touch ~/.Renviron` - `R_LIBS_USER` in `~/.Renviron`. Example: ```{bash} cat ~/.Renviron # Set local library installation path R_LIBS_USER=/gscratch/srlab/${USER}/R_libs_apptainer ``` ::: This configuration directs R to install and access packages from a custom directory rather than the system-wide library, which is especially useful in shared or containerized environments. # SLURM JOB SCRIPT ```{bash} cp ../sr320/rstudio-server.job . ``` ::: callout-warning - User needs to (maybe) set/change the following in the SLURM script before starting script: - `#SBATCH --partition=` - `#SBATCH --time=` - `#SBATCH --cpus-per-task=` - `#SBATCH --mem=` - `#SBATCH --chdir=` - `RSTUDIO_CWD="/gscratch/srlab/sr320" # UPDATE THIS LINE` - `RSTUDIO_SIF="srlab-R4.4-bioinformatics-container-703094b.sif" # UPDATE THIS LINE` ::: ## Partition Options `cpu-g2-mem2x` or `ckpt` ```{bash} [sr320@klone-login03 containers]$ hyakalloc Account resources available to user: sr320 ╭─────────┬──────────────┬──────┬────────┬──────┬───────╮ │ Account │ Partition │ CPUs │ Memory │ GPUs │ │ ├─────────┼──────────────┼──────┼────────┼──────┼───────┤ │ srlab │ cpu-g2-mem2x │ 32 │ 490G │ 0 │ TOTAL │ │ │ │ 12 │ 100G │ 0 │ USED │ │ │ │ 20 │ 390G │ 0 │ FREE │ ╰─────────┴──────────────┴──────┴────────┴──────┴───────╯ Checkpoint Resources (ckpt) ╭───────┬──────┬──────╮ │ │ CPUs │ GPUs │ ├───────┼──────┼──────┤ │ Idle: │ 4557 │ 148 │ ╰───────┴──────┴──────╯ ``` Open ```{bash} nano rstudio-server.job ``` ```{bash} #!/bin/sh #SBATCH --job-name=rstudio-server #SBATCH --account=srlab #SBATCH --partition=cpu-g2-mem2x #update this line - use hyakalloc to find partitions you can use #SBATCH --time=15-08:00:00 #SBATCH --ntasks=1 # Number of tasks #SBATCH --cpus-per-task=12 # Increased threads from 4 to 8 #SBATCH --nodes=1 #SBATCH --mem=100G #SBATCH --signal=USR2 #SBATCH --output=%x_%j.out ## Specify the working directory for this job #SBATCH --chdir=/gscratch/srlab/sr320 # This script will request a single CPU with four threads with 20GB of RAM for 2 hours. # You can adjust --time, --nodes, --ntasks, and --mem above to adjust these settings for your session. # --output=%x_%j.out creates a output file called rstudio-server_NNNNNNNN.out # where the %x is short hand for --job-name above and the N's are an 8-digit # jobID assigned by SLURM when our job is submitted. RSTUDIO_CWD="/gscratch/srlab/sr320" # UPDATE THIS LINE RSTUDIO_SIF="srlab-R4.4-bioinformatics-container-703094b.sif" # UPDATE THIS LINE # Create temp directory for ephemeral content to bind-mount in the container RSTUDIO_TMP=$(/usr/bin/python3 -c 'import tempfile; print(tempfile.mkdtemp())') mkdir -p -m 700 \ ${RSTUDIO_TMP}/run \ ${RSTUDIO_TMP}/tmp \ ${RSTUDIO_TMP}/var/lib/rstudio-server cat > ${RSTUDIO_TMP}/database.conf <<END provider=sqlite directory=/var/lib/rstudio-server END # Set OMP_NUM_THREADS to prevent OpenBLAS (and any other OpenMP-enhanced # libraries used by R) from spawning more threads than the number of processors # allocated to the job. # # Set R_LIBS_USER to a path specific to rocker/rstudio to avoid conflicts with # personal libraries from any R installation in the host environment cat > ${RSTUDIO_TMP}/rsession.sh <<END #!/bin/sh export OMP_NUM_THREADS=${SLURM_JOB_CPUS_PER_NODE} export R_LIBS_USER=${RSTUDIO_CWD}/R exec /usr/lib/rstudio-server/bin/rsession "\${@}" END chmod +x ${RSTUDIO_TMP}/rsession.sh export APPTAINER_BIND="${RSTUDIO_CWD}:${RSTUDIO_CWD},/gscratch:/gscratch,${RSTUDIO_TMP}/run:/run,${RSTUDIO_TMP}/tmp:/tmp,${RSTUDIO_TMP}/database.conf:/etc/rstudio/database.conf,${RSTUDIO_TMP}/rsession.sh:/etc/rstudio/rsession.sh,${RSTUDIO_TMP}/var/lib/rstudio-server:/var/lib/rstudio-server" # Do not suspend idle sessions. # Alternative to setting session-timeout-minutes=0 in /etc/rstudio/rsession.conf export APPTAINERENV_RSTUDIO_SESSION_TIMEOUT=0 export APPTAINERENV_USER=$(id -un) export APPTAINERENV_PASSWORD=$(openssl rand -base64 15) # get unused socket per https://unix.stackexchange.com/a/132524 # tiny race condition between the python & apptainer commands readonly PORT=$(/mmfs1/sw/pyenv/versions/3.9.5/bin/python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()') cat 1>&2 <<END 1. SSH tunnel from your workstation using the following command: ssh -N -L 8787:${HOSTNAME}:${PORT} ${APPTAINERENV_USER}@klone.hyak.uw.edu and point your web browser to http://localhost:8787 2. log in to RStudio Server using the following credentials: user: ${APPTAINERENV_USER} password: ${APPTAINERENV_PASSWORD} When done using RStudio Server, terminate the job by: 1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window) 2. Issue the following command on the login node: scancel -f ${SLURM_JOB_ID} END source /etc/bashrc module load apptainer apptainer exec --cleanenv --home ${RSTUDIO_CWD} ${RSTUDIO_CWD}/${RSTUDIO_SIF} \ rserver --www-port ${PORT} \ --auth-none=0 \ --auth-pam-helper-path=pam-helper \ --auth-stay-signed-in-days=30 \ --auth-timeout-minutes=0 \ --rsession-path=/etc/rstudio/rsession.sh \ --server-user=${APPTAINERENV_USER} APPTAINER_EXIT_CODE=$? echo "rserver exited $APPTAINER_EXIT_CODE" 1>&2 exit $APPTAINER_EXIT_CODE ``` # Run ```{bash} sbatch rstudio-server.job ``` # Folllow Instructions in output file to connect to RStudio. eg ```{bash} 1. SSH tunnel from your workstation using the following command: ssh -N -L 8787:n3263:56093 sr320@klone.hyak.uw.edu and point your web browser to http://localhost:8787 2. log in to RStudio Server using the following credentials: user: sr320 password: PDQlr876755PgP3g37c When done using RStudio Server, terminate the job by: 1. Exit the RStudio Session ("power" button in the top right corner of the RStudio window) 2. Issue the following command on the login node: scancel -f 24359989 ``` # Footnotes ``` srlab-bioinformatics-container-<git commit hash>.sif: A "catch-all" container which holds most of the commonly used bioinformatics software used by the Roberts Lab. The <git commit hash> is taken from the definition file used to construct the container. The definition file can be found at /gscratch/srlab/gitrepos/RobertsLab/code/apptainer_definition_files/srlab-bioinformatics-container.def. ``` ## Definition File ```{bash} [sr320@klone-login03 containers]$ cat /gscratch/srlab/gitrepos/RobertsLab/code/apptainer_definition_files/srlab-bioinformatics-container.def ``` ```{bash} # NOTE: # To use RepeatMasker with this container, RepeatMasker must be installed on the local computer in the following location: # # /gscratch/srlab/programs/RepeatMasker # # RepeatMasker must be configured on the local computer prior to running via this container. # The container expects the following files: # # /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/dfam38_full.0.h5 # /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/rmlib.config Bootstrap: docker From: rocker/rstudio:4.4.1 %files # Load file with R package installation commands in to container at /tmp # Expects file called "r_packages_installs.R" to be in current directory. r_packages_installs.R /tmp/ %setup %environment ### Set program locations/versions for system PATH ### programs_location="/srlab/programs" bismark_version="0.24.2" bowtie2_version="2.5.4" diamond_version="2.1.9" fastp_version="0.23.4" fastqc_version="0.12.1" gffcompare_version="gffcompare-0.12.6" hisat2_version="2.2.1" kallisto_version="0.51.1" miniforge_version="24.7.1-0" multiqc_version="1.24.1" ncbi_blast_version="2.16.0" ncbi_datasets_version="13.34.0" repeatmasker_version="4.1.7-p1" rmblast_version="2.14.1" salmon_version="1.10.0" samtools_version="1.20" stringtie_version="2.2.1" trimmomatic_version="0.39" mamba_envs_dir="${programs_location}/miniforge3-${miniforge_version}/envs" ###################################################### export LC_ALL=C ### Set container system PATH ### PATH="/usr/local/sbin:\ /usr/local/bin:\ /usr/sbin:\ /usr/bin:\ /sbin:\ /bin:\ ${programs_location}:\ ${programs_location}/Bismark-${bismark_version}:\ ${programs_location}/bowtie2-${bowtie2_version}-sra-linux-x86_64:\ ${programs_location}/fastqc-${fastqc_version}:\ ${programs_location}/${gffcompare_version}:\ ${programs_location}/hisat2-${hisat2_version}:\ ${programs_location}/kallisto-${kallisto_version}/build/src:\ ${programs_location}/miniforge3-${miniforge_version}/bin:\ ${mamba_envs_dir}/multiqc_env/bin:\ ${programs_location}/ncbi-blast-${ncbi_blast_version}+/bin:\ ${programs_location}/ncbi-datasets-${ncbi_datasets_version}:\ ${programs_location}/RepeatMasker:\ ${programs_location}/rmblast-${rmblast_version}/bin:\ ${programs_location}/salmon-latest_linux_x86_64/bin:\ ${programs_location}/samtools-${samtools_version}:\ ${programs_location}/stringtie-${stringtie_version}.Linux_x86_64:\ ${programs_location}/Trimmomatic-${trimmomatic_version}:\ ${programs_location}/trf409.linux64" ###################################################### %post # Install common/base libraries/dependencies apt update && \ apt install -y --no-install-recommends \ apt-utils \ aptitude \ automake \ build-essential \ bzip2 \ cmake \ coreutils \ curl \ debconf \ default-jdk \ dialog \ emboss \ gcc-multilib \ gdebi-core \ gfortran \ git \ gobjc++ \ hmmer \ htop \ infernal \ libapparmor1 \ libbz2-dev \ libc6 \ libcurl4-openssl-dev \ libedit2 \ libfontconfig1 \ liblzma-dev \ libncurses5-dev \ libncurses-dev \ libncursesw5-dev \ libpango1.0-dev \ libpng-dev \ libreadline-dev \ libsm6 \ libsparsehash-dev \ libssl-dev \ liburi-escape-xs-perl \ liburi-perl \ libxml2 \ libxrender1 \ libz-dev \ libbz2-dev \ liblzma-dev \ libxt6 \ libxtst6 \ libzmq3-dev \ locales \ locales-all \ man \ nano \ ncurses-dev \ net-tools \ openssh-client \ parallel \ pkg-config \ psmisc \ python3 \ python-setuptools \ rsync \ ruby \ software-properties-common \ sqlite3 \ sudo \ texinfo \ tree \ unzip \ wget \ xorg-dev \ zlib1g-dev # Run R package installation script file Rscript /tmp/r_packages_installs.R ########## Set program versions ########## bedtools_version="v2.31.0" bismark_version="0.24.2" bowtie2_version="2.5.4" diamond_version="2.1.9" fastp_version="0.23.4" fastqc_version="0.12.1" gffcompare_version="gffcompare-0.12.6" hisat2_version="2.2.1" kallisto_version="0.51.1" miniforge_version="24.7.1-0" multiqc_version="1.24.1" ncbi_blast_version="2.16.0" ncbi_datasets_version="16.34.0" repeatmasker_version="4.1.7-p1" rmblast_version="2.14.1" salmon_version="1.10.0" stringtie_version="2.2.1" samtools_version="1.20" trimmomatic_version="0.39" ########################################## # Set threads for faster builds threads="40" # Make programs directory mkdir --parents /srlab/programs # Change to installation directory cd /srlab/programs #Install Miniforge (Conda/Mamba) wget https://github.com/conda-forge/miniforge/releases/download/${miniforge_version}/Miniforge3-${miniforge_version}-Linux-x86_64.sh bash Miniforge3-${miniforge_version}-Linux-x86_64.sh -b -p ./miniforge3-${miniforge_version} export PATH="$PATH:/srlab/programs/miniforge3-${miniforge_version}/bin" mamba init . ./miniforge3-${miniforge_version}/etc/profile.d/conda.sh rm Miniforge3-${miniforge_version}-Linux-x86_64.sh ## Configure conda channels conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict # Install bedtools wget https://github.com/arq5x/bedtools2/releases/download/${bedtools_version}/bedtools.static mv bedtools.static bedtools chmod a+x bedtools # Install Bismark wget https://github.com/FelixKrueger/Bismark/archive/refs/tags/v${bismark_version}.zip unzip v${bismark_version}.zip rm v${bismark_version}.zip # Install bowtie2 wget https://github.com/BenLangmead/bowtie2/releases/download/v${bowtie2_version}/bowtie2-${bowtie2_version}-sra-linux-x86_64.zip unzip bowtie2-${bowtie2_version}-sra-linux-x86_64.zip rm bowtie2-${bowtie2_version}-sra-linux-x86_64.zip # Install DIAMOND BLAST wget https://github.com/bbuchfink/diamond/releases/download/v${diamond_version}/diamond-linux64.tar.gz tar -xzvf diamond-linux64.tar.gz rm diamond-linux64.tar.gz # Install fastp wget http://opengene.org/fastp/fastp.${fastp_version} mv fastp.${fastp_version} fastp chmod a+x ./fastp # Install FastQC wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${fastqc_version}.zip unzip fastqc_v${fastqc_version}.zip mv FastQC fastqc-${fastqc_version} rm fastqc_v${fastqc_version}.zip # Install gffcompare wget http://ccb.jhu.edu/software/stringtie/dl/${gffcompare_version}.Linux_x86_64.tar.gz tar -xzvf ${gffcompare_version}.Linux_x86_64.tar.gz rm ${gffcompare_version}.Linux_x86_64.tar.gz # Install HISAT2 wget https://github.com/DaehwanKimLab/hisat2/archive/refs/tags/v${hisat2_version}.tar.gz tar -xzvf v${hisat2_version}.tar.gz cd hisat2-${hisat2_version} make -j ${threads} cd - rm v${hisat2_version}.tar.gz # Install kallisto wget https://github.com/pachterlab/kallisto/archive/refs/tags/v${kallisto_version}.tar.gz tar -xzvf v${kallisto_version}.tar.gz cd kallisto-${kallisto_version} mkdir build cd build cmake .. make cd /srlab/programs rm v${kallisto_version}.tar.gz # Install MultiQC mamba create -n multiqc_env multiqc=1.24.1 # Install NCBI datasets mkdir --parents ncbi-datasets-v${ncbi_datasets_version} cd ncbi-datasets-v${ncbi_datasets_version} wget https://github.com/ncbi/datasets/releases/download/v16.34.0/linux-amd64.cli.package.zip \ && unzip linux-amd64.cli.package.zip \ && rm linux-amd64.cli.package.zip cd /srlab/programs # Install NCBI BLAST wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${ncbi_blast_version}/ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz \ && tar -zxvpf ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz \ && rm ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz # RepeatMasker conda environment with Python3 and h5py using mamba mamba create -n repeatmasker-env python=3.8 h5py -y # Install RepeatMasker wget https://www.repeatmasker.org/RepeatMasker/RepeatMasker-${repeatmasker_version}.tar.gz tar -xzvf RepeatMasker-${repeatmasker_version}.tar.gz rm RepeatMasker-${repeatmasker_version}.tar.gz ## Remove default RepeatMasker DB rm /srlab/programs/RepeatMasker/Libraries/famdb/* # Set up symlinks to RepeatMasker files on Klone ln -s /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/dfam38_full.0.h5 /srlab/programs/RepeatMasker/Libraries/famdb/dfam38_full.0.h5 ln -s /gscratch/srlab/programs/RepeatMasker/Libraries/famdb/rmlib.config /srlab/programs/RepeatMasker/Libraries/famdb/rmlib.config # Install RMBLAST wget https://www.repeatmasker.org/rmblast/rmblast-${rmblast_version}+-x64-linux.tar.gz tar -xzvf rmblast-${rmblast_version}+-x64-linux.tar.gz rm rmblast-${rmblast_version}+-x64-linux.tar.gz # Install salmon wget https://github.com/COMBINE-lab/salmon/releases/download/v${salmon_version}/salmon-${salmon_version}_linux_x86_64.tar.gz tar -xzvf salmon-${salmon_version}_linux_x86_64.tar.gz rm salmon-${salmon_version}_linux_x86_64.tar.gz # Install samtools wget https://github.com/samtools/samtools/releases/download/${samtools_version}/samtools-${samtools_version}.tar.bz2 tar -xjvf samtools-${samtools_version}.tar.bz2 cd samtools-${samtools_version} ./configure make -j ${threads} cd - rm samtools-${samtools_version}.tar.bz2 # Install trimmomatic wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-${trimmomatic_version}.zip unzip Trimmomatic-${trimmomatic_version}.zip chmod +x -R Trimmomatic-${trimmomatic_version} rm Trimmomatic-${trimmomatic_version}.zip # Install StringTie wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-${stringtie_version}.Linux_x86_64.tar.gz tar -xzvf stringtie-${stringtie_version}.Linux_x86_64.tar.gz rm stringtie-${stringtie_version}.Linux_x86_64.tar.gz # Install TRF wget https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64 chmod +x trf409.linux64 %labels Author Sam White Version v0.0.5 %help This is an Apptainer definition file for an Ubuntu container containing bioinformatics software for the Roberts Lab. ```